Re: [GUSDEV] Regarding comment tables in the DoTS

[Bindu G. <bi...@pc...>]

Jian -
i dont think Ed mentioned explicitly how dots.nafeaturecomment is used.
here, we store the GenBank data comments in the dots.nacomment table.

Bindu


On Apr 26, 2005, at 12:42 PM, Jian Lu wrote:

> As Ed mentioned, that dots.nafeaturecomment is also used for storing 
> GenBank data comment . If I insert a new comment to 
> dots.nafeaturecomment table with the same fk na_feature_id, how could 
> I tell which one is which by query? (assuming there has been GenBank 
> comment)
>
> Thanks,
> Jian
>
> Bindu Gajria wrote:
>
>> dots.nafeaturecomment table has the field na_feature_id, which is a 
>> foreign key. plasmodium gene features are stored in dots.genefeature, 
>> whose primary key is na_feature_id. so, one can identify the comment 
>> in the nafeaturecomment table to a particular gene.
>>
>> bindu
>>
>> On Apr 26, 2005, at 11:45 AM, Jian Lu wrote:
>>
>>> Thank you all.
>>>
>>> By using dots.nafeaturecomment table, how could you tell the 
>>> comments from GenBank file or curators or other results?
>>>
>>> Jian
>>>
>>> Bindu Gajria wrote:
>>>
>>>> hi Jian -
>>>> appending to Ed's reply:
>>>> to help in curation, we have set up a mechanism in PlasmoDB to 
>>>> allow for the user community to submit (and view) comments on 
>>>> genes. and for this, PlasmoDB uses dots.nafeaturecomment table. 
>>>> will be glad to provide specifics on how this table, or the others 
>>>> are used.
>>>>
>>>> Bindu
>>>>
>>>>
>>>> On Apr 26, 2005, at 10:09 AM, Ed Robinson wrote:
>>>>
>>>>> Curation is something we are still/constantly incorporating
>>>>> into GUS.  If you can give us more information about your
>>>>> specific curatorial needs, a number of people here can point
>>>>> you to the best places to locate that information.
>>>>>
>>>>> Generally, the comment fields you are talking about are not
>>>>> used for curatorial purposes, but are used for capturing
>>>>> annotations loaded from input files such as GenBank.  For
>>>>> instance,  a comment in the header of a GenBank file would
>>>>> likely go in the comment section, a commnet or note in a gene
>>>>> feature would go in an NAComment and a comment or note in a
>>>>> CDS feature would go in an AAComment.  Of course, the tables
>>>>> you mention AAFeatureImp and NAFeatureImp are not themselves
>>>>> tables you would use directly.  Rather, you would use specific
>>>>> feature views of these tables, such as GeneFeature, Transcript
>>>>> and TranslatedAAFeature.
>>>>>
>>>>> Of course, none of this should stop you from using these
>>>>> tables in the ways that seem best for your data.  If you want
>>>>> to add free-form notes to features, these tables are are
>>>>> likely one of the better places.
>>>>>
>>>>> In general, curatorial information is found in the SRes
>>>>> tables, so you should look at those closely also.
>>>>>
>>>>> Also, you should dig around in the documentation section of
>>>>> gusdb.org.  There are some papers that discuss the schema
>>>>> buried somewhere in there.
>>>>>
>>>>> -ed
>>>>>
>>>>>
>>>>>
>>>>> ---- Original message ----
>>>>>
>>>>>> Date: Mon, 25 Apr 2005 12:11:28 -0400
>>>>>> From: Jian Lu <jl...@vb...>
>>>>>> Subject: [GUSDEV] Regarding comment tables in the DoTS
>>>>>> To: gus...@li...
>>>>>>
>>>>>> Hi GUS folks,
>>>>>>
>>>>>> I am new in GUS schema. This might not be a new question, but I 
>>>>>> just
>>>>>> want to understand more about GUS. It would be great  if someone 
>>>>>> already
>>>>>> has had answers.
>>>>>>
>>>>>> I realize that there are different comment tables at DoTS:
>>>>>>
>>>>>> COMMENTS (COMMENTS_ID, COMMENT_STRING, REVIEW_STATUS_ID, ...)
>>>>>>
>>>>>> AACOMMENT (AA_COMMENT_ID, AA_SEQUENCE_ID, COMMENT_NAME_ID,
>>>>>> COMMENT_STRING, ...)
>>>>>>
>>>>>> NACOMMENT (NA_COMMENT_ID, NA_SEQUENCE_ID, COMMENT_STRING, ...)
>>>>>>
>>>>>> They have all common attributes (comment_id and comment_string), 
>>>>>> and AA
>>>>>> and NA groups have their associated sequence_ids. However, the
>>>>>> differences are obvious that REVIEW_STATUS_ID only at the COMMENTS
>>>>>> table, and COMMENT_NAME_ID only exists at the AACOMMENT table.
>>>>>>
>>>>>> Also, there is a NAFEATURECOMMENT table associated with 
>>>>>> NAFEATUREIMP
>>>>>> table. But there is no such table for AAFEATUREIMP.
>>>>>> If there would be comments on a feature, where should they go?
>>>>>>
>>>>>> The reason I brought this issue is we are considering to use 
>>>>>> comment
>>>>>> tables to store curation evidence and knowledge content, and we 
>>>>>> want to
>>>>>> make our development consistent.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jian Lu
>>>>>> VBI
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>
>>>>> -----------------
>>>>> Ed Robinson
>>>>> Center for Tropical and Emerging Global Diseases
>>>>> University of Georgia, Athens, GA 30602
>>>>> ero...@ug.../(706)542.1447/254.8883
>>>>>
>>>>>
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